From 00a63e0a478d4f7527d587a458cf4ff62f578fba Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:28:06 +0100 Subject: [PATCH] =?UTF-8?q?Serialisation=20prot=C3=A9g=C3=A9=205.6.3=20(#3?= =?UTF-8?q?085)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Serialisation protégé 5.6.3 Serialisation protégé 5.6.3 * odd serialisation in annotation IAO:0000116 (editor notes) * change `IAO:0000116` to `rdfs:comment` * use `notes` in the case of multiple comment tags * add `notes` to accepted annotations list * change to `notes` another case multiple comment tag * use `curator_notes` instead of `notes` * fix comment OBO syntax * add EDITOR_NOTE to comments previously from `editor notes` annotation * replace `UBPROP:0000008` and `IAO:0000232` with `comment` when annotation in another axiom * normalize uberon-edit file --------- Co-authored-by: Anita Caron Co-authored-by: Anita Caron --- src/ontology/uberon-edit.obo | 94 ++++++++++++++++++------------------ 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 60339f803e..03c4879b1c 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -56,11 +56,11 @@ treat-xrefs-as-equivalent: VSAO treat-xrefs-as-is_a: VHOG remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found. import: http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl +import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl import: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl import: http://purl.obolibrary.org/obo/uberon/components/mappings.owl import: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl -import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl import: http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl import: http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl ontology: uberon/core @@ -928,7 +928,7 @@ intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha -relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} ! Otomorpha +relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} ! Nematoda relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} ! Dipnomorpha @@ -7753,7 +7753,7 @@ xref: ENVO:02000026 xref: FMA:62961 xref: Wikipedia:Chyme is_a: UBERON:0006314 {source="WP"} ! bodily fluid -is_a: UBERON:0012112 {editor_note="consider changing to derivation relationship", source="FMA"} ! ingested food +is_a: UBERON:0012112 {source="FMA", comment="consider changing to derivation relationship"} ! ingested food disjoint_from: UBERON:0012113 ! bolus of food relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! acidic relationship: located_in UBERON:0004908 ! upper digestive tract @@ -10362,6 +10362,7 @@ property_value: taxon_notes "Most vertebrates have some form of duct to transfer id: UBERON:0001001 name: chitin-based cuticle def: "A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/index.php?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Arthropod_exoskeleton, Wikipedia:Cuticle#Invertebrate_zoology] +comment: EDITOR_NOTE TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO subset: efo_slim subset: uberon_slim synonym: "arthropod cuticle" RELATED [] @@ -10379,12 +10380,12 @@ intersection_of: composed_primarily_of CHEBI:17029 ! chitin relationship: develops_from UBERON:0007376 ! outer epithelium relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0002416 ! integumental system -property_value: editor_note "TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO" xsd:string [Term] id: UBERON:0001002 name: cuticle def: "Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP]." [http://sourceforge.net/tracker/?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Cuticle] +comment: EDITOR_NOTE TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part subset: grouping_class subset: non_informative subset: uberon_slim @@ -10395,7 +10396,6 @@ xref: Wikipedia:Cuticle is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0004882 ! eponychium relationship: only_in_taxon NCBITaxon:6072 {source="Rieger - Evolution of the Cuticle in the Lower Eumetazoa"} ! Eumetazoa -property_value: editor_note "TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part" xsd:string property_value: has_relational_adjective "cuticular" xsd:string [Term] @@ -10592,6 +10592,7 @@ property_value: has_relational_adjective "digestive" xsd:string id: UBERON:0001008 name: renal system def: "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products." [DOI:10.1371/journal.pone.0099864, GO:0072001] +comment: EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -10636,7 +10637,6 @@ relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: editor_note "In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here" xsd:string property_value: external_definition "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} property_value: taxon_notes "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} @@ -10962,6 +10962,7 @@ property_value: external_definition "White matter structure of CNS that contains id: UBERON:0001019 name: nerve fasciculus def: "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." [BIRNLEX:872, FBbt:00005101] +comment: EDITOR_NOTE note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle' subset: uberon_slim synonym: "fascicle" BROAD [FBbt:00005101] synonym: "fasciculus" EXACT LATIN [] @@ -10978,7 +10979,6 @@ xref: TGMA:0000088 xref: UMLS:C1185741 {source="ncithesaurus:Fascicle"} xref: Wikipedia:Nervous_system_fascicle is_a: UBERON:0000122 ! neuron projection bundle -property_value: editor_note "note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'" xsd:string [Term] id: UBERON:0001020 @@ -11839,6 +11839,7 @@ property_value: external_ontology_notes "currently intended for invert structure id: UBERON:0001054 name: Malpighian tubule def: "A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified]." [Wikipedia:Malpighian_tubule_system] +comment: EDITOR_NOTE this will be ceded to the Arthropod Anatomy Ontology subset: efo_slim subset: uberon_slim synonym: "Malphigian tube" RELATED MISSPELLING [BTO:0000810] @@ -11856,7 +11857,6 @@ xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda -property_value: editor_note "this will be ceded to the Arthropod Anatomy Ontology" xsd:string property_value: taxon_notes "It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]" xsd:string [Term] @@ -12012,6 +12012,7 @@ id: UBERON:0001064 name: ventral pancreatic duct alt_id: UBERON:0005627 def: "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct] +comment: EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue subset: uberon_slim synonym: "canal of Wirsung" RELATED [BTO:0002362] synonym: "chief pancreatic duct" EXACT [FMA:16003] @@ -12042,13 +12043,13 @@ relationship: develops_from UBERON:0003924 {source="EHDAA2"} ! ventral pancreati relationship: part_of UBERON:0000017 ! exocrine pancreas property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI property_value: development_notes "Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct." xsd:string {source="WP"} -property_value: editor_note "in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue" xsd:string property_value: homology_notes "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000256", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001065 name: parotid main excretory duct def: "The main excretory tubular canal that connects the parotid gland and the buccal mucosa and secretes a serous saliva into the vestibule of the oral cavity; it arises from the anterior surface of the gland, traversing the masseter muscle; the duct then pierces the buccinator muscle, moving medially, and opens out into the oral cavity near the second upper molar; saliva produced by acinar secretory cells in the glandular body flows sequentially through the intercalated ducts, striated ducts, and excretory ducts." [MP:0009530] +comment: EDITOR_NOTE we follow MP in identifying the 'parotid duct' with the main excretory duct, although in fact the parotid has many other ducts of different types subset: pheno_slim subset: uberon_slim synonym: "duct of parotid" BROAD [OBOL:automatic] @@ -12078,7 +12079,6 @@ relationship: channels_from UBERON:0001831 ! parotid gland relationship: contributes_to_morphology_of UBERON:0001831 ! parotid gland relationship: part_of UBERON:0001831 ! parotid gland property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1023.png" xsd:anyURI -property_value: editor_note "we follow MP in identifying the 'parotid duct' with the main excretory duct, although in fact the parotid has many other ducts of different types" xsd:string [Term] id: UBERON:0001066 @@ -12140,6 +12140,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gr id: UBERON:0001068 name: skin of back def: "A zone of skin that is part of a back [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region subset: pheno_slim synonym: "back skin" EXACT [] synonym: "back zone of skin" EXACT [OBOL:automatic] @@ -12154,7 +12155,6 @@ is_a: UBERON:0001085 {source="MA"} ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0011270 {source="MA"} ! dorsal trunk -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001069 @@ -12440,6 +12440,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Pe id: UBERON:0001079 name: prezygapophysis def: "Paired processes at the cephalic end of the neural arch. The articular facets of the prezygapophyses face dorsomedially and articulate with the lateroventrally facing facets of the postzygapophyses of the preceding vertebra." [AAO:Pugener_and_Maglia_2008] +comment: EDITOR_NOTE TODO - add distinct classes for hemal vs neural? subset: vertebrate_core synonym: "cranial articular process of vertebra" EXACT [] synonym: "neural prezygapophyses" RELATED PLURAL [TAO:0001325] @@ -12460,7 +12461,6 @@ xref: SCTID:42424006 xref: TAO:0001325 xref: ZFA:0001325 is_a: UBERON:0006062 ! zygapophysis -property_value: editor_note "TODO - add distinct classes for hemal vs neural?" xsd:string property_value: external_definition "Paired, anteromedially directed processes from the neural arches, ligamentously joined to the postzygapophyses of the preceding vertebra.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001325", ontology="TAO", source="ZFIN:curator"} [Term] @@ -12568,6 +12568,7 @@ property_value: homology_notes "As noted, the hearts of birds and mammals have f id: UBERON:0001084 name: skin of head def: "A zone of skin that is part of a head [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region synonym: "adult head zone of skin" EXACT [OBOL:automatic] synonym: "head skin" EXACT [] synonym: "head zone of skin" EXACT [OBOL:automatic] @@ -12582,12 +12583,12 @@ xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000033 ! head -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001085 name: skin of trunk def: "A zone of skin that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region synonym: "torso zone of skin" EXACT [OBOL:automatic] synonym: "trunk skin" EXACT [] synonym: "trunk zone of skin" EXACT [OBOL:automatic] @@ -12603,7 +12604,6 @@ xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002100 ! trunk -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001086 @@ -12708,6 +12708,7 @@ property_value: structure_notes "The fluid contains hyaluronan secreted by fibro id: UBERON:0001091 name: calcareous tooth def: "Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Tooth_(animal)] +comment: EDITOR_NOTE we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -12750,7 +12751,6 @@ relationship: never_in_taxon NCBITaxon:9257 {source="PMID:10210685"} ! Ornithorh relationship: never_in_taxon NCBITaxon:9761 ! Mysticeti relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI -property_value: editor_note "we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures" xsd:string property_value: has_relational_adjective "dental" xsd:string property_value: homology_notes "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001733", ontology="VHOG", source="PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)", source="http://bgee.unil.ch/"} property_value: taxon_notes "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni" xsd:string {source="PMID:10210685"} @@ -12833,6 +12833,7 @@ property_value: vertebra_number "2" xsd:nonNegativeInteger id: UBERON:0001094 name: sacral vertebra def: "A vertebra bone that is part of the sacral region of the vertebral column." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs) subset: pheno_slim subset: uberon_slim synonym: "sacral segment" EXACT [] @@ -12851,7 +12852,6 @@ xref: XAO:0003078 intersection_of: UBERON:0015010 ! sacral vertebra endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010745 ! sacral vertebra cartilage element -property_value: editor_note "todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs)" xsd:string property_value: external_definition "Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000552", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] @@ -15950,7 +15950,7 @@ xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} ! Testudines relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota -relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria +relationship: part_of UBERON:0000030 {comment="EDITOR_NOTE check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"} property_value: external_ontology_notes "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"} @@ -22424,7 +22424,7 @@ relationship: preaxialmost_part_of UBERON:0002398 ! manus property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2c/Thumbs_up.jpg" xsd:anyURI property_value: taxon_notes "Not present in Anurans (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012260", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"} [Term] id: UBERON:0001464 @@ -28122,7 +28122,7 @@ relationship: part_of UBERON:0010272 ! hyoid apparatus property_value: axiom_lost_from_external_ontology "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI property_value: external_definition "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO", source="AAO:LAP"} -property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/548", source="WP"} +property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"} [Term] id: UBERON:0001686 @@ -34096,7 +34096,7 @@ xref: VHOG:0001625 xref: Wikipedia:Olfactory_tubercle is_a: UBERON:0000125 {source="EHDAA2"} ! neural nucleus relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex -relationship: dubious_for_taxon NCBITaxon:9443 {editor_note="check EHDAA2", source="MP"} ! Primates +relationship: dubious_for_taxon NCBITaxon:9443 {source="MP", comment="EDITOR_NOTE check EHDAA2"} ! Primates relationship: mutually_spatially_disjoint_with UBERON:0001882 {source="ABA"} ! nucleus accumbens relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex relationship: part_of UBERON:0005401 {source="BTO"} ! cerebral hemisphere gray matter @@ -35075,7 +35075,7 @@ xref: Wikipedia:Pineal_gland xref: XAO:0000160 xref: ZFA:0000019 is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ -relationship: capable_of GO:0030187 {editor_note="add secretion"} ! melatonin biosynthetic process +relationship: capable_of GO:0030187 {comment="EDITOR_NOTE add secretion"} ! melatonin biosynthetic process relationship: contributes_to_morphology_of UBERON:0001899 ! epithalamus relationship: has_part CL:0000652 ! pinealocyte relationship: has_part CL:0002220 ! interstitial cell of pineal gland @@ -38620,7 +38620,7 @@ xref: Wikipedia:Spinal_accessory_nerve xref: XAO:0004214 intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus -relationship: dubious_for_taxon NCBITaxon:8292 {seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7", source="VHOG", source="Wikipedia"} ! Amphibia +relationship: dubious_for_taxon NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia relationship: innervates UBERON:0001737 ! larynx relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda @@ -44581,7 +44581,7 @@ xref: Wikipedia:Nerve_root is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001021 ! nerve -relationship: part_of UBERON:0001016 {editor_note="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system +relationship: part_of UBERON:0001016 {comment="EDITOR_NOTE we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system property_value: editor_note "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string property_value: external_definition "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." xsd:string {source="FBbt:00007602, FBC:DOS"} property_value: external_ontology_notes "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" xsd:string {external_ontology="FMA"} @@ -45475,7 +45475,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Ce id: UBERON:0002246 name: dorsal thoracic nucleus def: "Two column-shaped nuclear masses formed by large cells. Clarke's nuclei are located in the regions dorsolateral to the central canal in the thoratic and upper lumbar segments." [NLXANAT:20090102] -comment: "Created by Sarah M. Maynard" xsd:string +comment: Created by Sarah M. Maynard subset: uberon_slim synonym: "Clarke's column" EXACT [] synonym: "Clarke's nuclei" RELATED PLURAL [NLXANAT:20090102] @@ -47106,6 +47106,7 @@ property_value: taxon_notes "the basic trilaminar structure of the dentate gyrus id: UBERON:0002305 name: layer of hippocampus def: "The layers of the laminar structure of the hippocampus." [MP:0000813, Wikipedia:Hippocampus_anatomy#Hippocampal_Cells_and_Layers] +comment: EDITOR_NOTE TODO - check NIF xref subset: pheno_slim synonym: "cytoarchitectural fields of hippocampal formation" EXACT [BIRNLEX:1192] synonym: "hippocampus layer" EXACT [] @@ -47120,12 +47121,12 @@ xref: Wikipedia:Hippocampus_anatomy#Hippocampal_Cells_and_Layers intersection_of: UBERON:0016548 ! central nervous system gray matter layer intersection_of: part_of UBERON:0002421 ! hippocampal formation relationship: contributes_to_morphology_of UBERON:0002421 ! hippocampal formation -property_value: editor_note "TODO - check NIF xref" xsd:string [Term] id: UBERON:0002306 name: nasal mucus def: "Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE TODO - split nasal vs respiratory tract? subset: uberon_slim synonym: "respiratory mucus" RELATED [BTO:0003603] xref: BTO:0003603 @@ -47138,7 +47139,6 @@ xref: UMLS:C0225392 {source="ncithesaurus:Nasal_Mucus"} xref: Wikipedia:Nasal_mucus#Respiratory_system intersection_of: UBERON:0000912 ! mucus intersection_of: produced_by UBERON:0015786 ! respiratory segment of nasal mucosa -property_value: editor_note "TODO - split nasal vs respiratory tract?" xsd:string property_value: function_notes "protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons" xsd:string [Term] @@ -47263,6 +47263,7 @@ id: UBERON:0002313 name: hippocampus pyramidal layer alt_id: UBERON:0005369 def: "A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames)." [BIRNLEX:1444] +comment: EDITOR_NOTE this layer changes in its depthwise spatial relation across its extent subset: pheno_slim synonym: "gyrus occipitalis inferior" RELATED LATIN [NeuroNames:156] synonym: "gyrus occipitalis tertius" RELATED LATIN [NeuroNames:156] @@ -47285,7 +47286,6 @@ intersection_of: UBERON:0002305 ! layer of hippocampus intersection_of: deep_to UBERON:0007637 ! hippocampus stratum lucidum intersection_of: immediately_superficial_to UBERON:0005371 ! hippocampus stratum oriens relationship: composed_primarily_of CL:0000598 ! pyramidal neuron -property_value: editor_note "this layer changes in its depthwise spatial relation across its extent" xsd:string [Term] id: UBERON:0002314 @@ -47498,6 +47498,7 @@ relationship: part_of UBERON:0004190 {source="GO"} ! renal glomerulus vasculatur id: UBERON:0002321 name: extraglomerular mesangium def: "The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus." [ISBN:0-683-40008-8, MP:0011340] +comment: EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? subset: pheno_slim xref: EMAPA:28278 xref: FMA:84141 @@ -47507,7 +47508,6 @@ relationship: overlaps UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0001229 {source="MA"} ! renal corpuscle relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0002319 {source="MA"} ! mesangium -property_value: editor_note "check MA part_ofs - should be spatially disjoint from renal glomerulus?" xsd:string [Term] id: UBERON:0002322 @@ -47529,6 +47529,7 @@ id: UBERON:0002323 name: coelemic cavity lumen alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] +comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim subset: vertebrate_core synonym: "body cavity" BROAD [BTO:0001707] @@ -47555,7 +47556,6 @@ xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: luminal_space_of UBERON:0011997 ! coelom relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: editor_note "check the FMA placement here; ncit placement of body cavity here probably not correct" xsd:string property_value: external_definition "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} property_value: external_definition "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} property_value: taxon_notes "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string @@ -47721,8 +47721,8 @@ relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: axiom_lost_from_external_ontology "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} +property_value: curator_notes "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: editor_note "currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string property_value: external_definition "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "somitic" xsd:string @@ -48075,9 +48075,9 @@ relationship: dubious_for_taxon NCBITaxon:117565 {source="ISBN:0073040584", sour relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm +property_value: curator_notes "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: editor_note "consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: external_definition "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} @@ -48188,6 +48188,7 @@ property_value: taxon_notes "Thoracic vertebrae in all species are defined as th id: UBERON:0002348 name: epicardium def: "A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -48211,7 +48212,6 @@ relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium relationship: develops_from UBERON:0004160 ! proepicardium relationship: part_of UBERON:0000948 {source="multiple"} ! heart relationship: part_of UBERON:0002425 {source="FMA-inferred"} ! visceral serous pericardium -property_value: editor_note "TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer." xsd:string property_value: external_definition "External layer of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005057", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010409", ontology="AAO", source="AAO:BJB"} property_value: function_notes "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]" xsd:string @@ -48220,6 +48220,7 @@ property_value: function_notes "The visceral pericardium apparently produces the id: UBERON:0002349 name: myocardium def: "The middle layer of the heart, comprised mainly of striated cardiac muscle fibers." [ISBN:0-683-40008-8, MP:0005329] +comment: EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -48257,7 +48258,6 @@ relationship: has_part UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0000383 ! musculature of body relationship: part_of UBERON:0000948 ! heart property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI -property_value: editor_note "TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium" xsd:string property_value: external_definition "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000083", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "The middle layer of the heart, consisting of cardiac muscle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010410", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "myocardial" xsd:string @@ -49719,6 +49719,7 @@ property_value: structure_notes "the nasolacrimal duct, the sac is lined by stra id: UBERON:0002393 name: pharyngotympanic tube def: "Organ with organ cavity which connects the cavity of the middle ear to the cavity of the pharynx. Examples: There are only two pharyngotympanic tubes, the right and the left pharyngotympanic tubes.[FMA]." [FMA:FMA, Wikipedia:Eustachian_tube] +comment: EDITOR_NOTE we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship subset: organ_slim subset: pheno_slim subset: uberon_slim @@ -49748,7 +49749,6 @@ relationship: has_part UBERON:0010062 ! pharyngotympanic tube epithelium relationship: part_of UBERON:0001756 ! middle ear property_value: axiom_lost_from_external_ontology "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000146", ontology="AAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Ear-anatomy-text-small-en.svg" xsd:anyURI -property_value: editor_note "we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship" xsd:string property_value: external_definition "Furrow on the ventral surface of the otic capsule, and occasionally also the parasphenoid, that houses the Eustachian tube.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000146", ontology="AAO", source="AAO:LAP"} property_value: external_definition "The narrow channel connecting the nasopharynx and the middle ear. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001145", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/auditory+tube"} property_value: homology_notes "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001145", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417", source="http://bgee.unil.ch/"} @@ -49952,6 +49952,7 @@ property_value: has_relational_adjective "manual" xsd:string id: UBERON:0002399 name: lesser omentum def: "The double layer of peritoneum that extends from the liver to the lesser curvature of the stomach and the start of the duodenum. [WP,unvetted]." [Wikipedia:Lesser_omentum] +comment: EDITOR_NOTE exact part of and develops from relationships need to be established subset: uberon_slim synonym: "gastrohepatic omentum" RELATED [Wikipedia:Lesser_omentum] synonym: "omentum minus" RELATED LATIN [Wikipedia:Lesser_omentum] @@ -49972,7 +49973,6 @@ relationship: develops_from UBERON:0005626 {source="EHDAA2", source="Wikipedia"} relationship: part_of UBERON:0001178 {source="FMA"} ! visceral peritoneum relationship: part_of UBERON:0005626 {source="MA"} ! ventral mesogastrium property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI -property_value: editor_note "exact part of and develops from relationships need to be established" xsd:string property_value: external_definition "A membranous extension of the peritoneum from the peritoneal layers covering the ventral and the dorsal surfaces of the stomach and the first part of the duodenum. The lesser omentum extends from the portal fissure of the liver to the diaphragm, where the layers separate to enclose the end of the esophagus. It also forms two ligaments, one associated with the liver, the hepatogastric ligament, and the other, the heptatoduodenal ligament, with the duodenum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000357", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lesser+omentum"} [Term] @@ -74714,7 +74714,7 @@ relationship: part_of UBERON:5003622 ! manual digit 2 plus metapodial segment property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d5/Index_finger.JPG" xsd:anyURI property_value: has_relational_adjective "indicis" xsd:string property_value: taxon_notes "Anurans lack manual digit 1, so manual digit 2 is the digit after the prepollex (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012261", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"} [Term] id: UBERON:0003623 @@ -74751,7 +74751,7 @@ relationship: ambiguous_for_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0012141 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! manual digitopodium region relationship: part_of UBERON:5003623 ! manual digit 3 plus metapodial segment property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/f/fd/Middle_finger.jpg" xsd:anyURI -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012262", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"} [Term] id: UBERON:0003624 @@ -76084,7 +76084,7 @@ xref: Wikipedia:Canine_tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: has_quality PATO:0005021 ! unicuspidate disjoint_from: UBERON:0007120 ! premolar tooth -relationship: has_part UBERON:0006844 {count="1", editor_note="cardinality not allowed with transitivity in OWL"} ! cusp of tooth +relationship: has_part UBERON:0006844 {count="1", comment="EDITOR_NOTE cardinality not allowed with transitivity in OWL"} ! cusp of tooth relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Azawakh_K9.jpg" xsd:anyURI @@ -76163,6 +76163,7 @@ relationship: part_of UBERON:0001091 ! calcareous tooth id: UBERON:0003679 name: mouth floor def: "The ventral area of the mouth. In organisms with a tongue, this is the area under the ventral surface of the tongue[ncit, modified]." [http://orcid.org/0000-0002-6601-2165, ncithesaurus:Floor_of_the_Mouth] +comment: EDITOR_NOTE reclassify after CARO2 overhaul subset: efo_slim subset: pheno_slim synonym: "floor of mouth" EXACT [FMA:86592] @@ -76180,7 +76181,6 @@ xref: SCTID:245786002 xref: UMLS:C0026638 {source="ncithesaurus:Floor_of_the_Mouth"} is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0000165 ! mouth -property_value: editor_note "reclassify after CARO2 overhaul" xsd:string [Term] id: UBERON:0003680 @@ -113228,7 +113228,7 @@ name: seminal fluid def: "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended." [http://orcid.org/0000-0002-6601-2165] synonym: "male genital fluid" RELATED [] synonym: "male genital secretion" RELATED [] -synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {http://purl.obolibrary.org/obo/IAO_0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} +synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {comment="CURATOR NOTE A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} synonym: "seminal fluid" RELATED [BTO:0001232] synonym: "seminal plasma" EXACT [BTO:0001232] xref: BTO:0001232 @@ -118700,7 +118700,7 @@ xref: SCTID:304572005 xref: UMLS:C1704302 {source="ncithesaurus:Bicuspid_Tooth"} xref: Wikipedia:Premolar is_a: UBERON:0013164 ! molariform tooth -relationship: has_part UBERON:0006844 {editor_note="cardinality not allowed with transitivity in OWL", min_count="2", taxon_notes="some premolars may have 3 cusps"} ! cusp of tooth +relationship: has_part UBERON:0006844 {min_count="2", comment="TAXON NOTE some premolars may have 3 cusps", comment="cardinality not allowed with transitivity in OWL"} ! cusp of tooth relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1003.png" xsd:anyURI property_value: taxon_notes "In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4" xsd:string @@ -139086,7 +139086,7 @@ name: spleen marginal sinus def: "The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood." [MP:MP] subset: pheno_slim synonym: "splenic marginal sinus" EXACT [MP:0002363] -xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"} +xref: EMAPA:37964 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"} xref: MA:0000754 xref: NCIT:C49776 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"} @@ -142049,7 +142049,7 @@ synonym: "ventral nasal capsule" EXACT [PMID:21270050] xref: AAO:0000303 is_a: UBERON:0010363 {source="TAO"} ! endochondral element relationship: develops_from UBERON:0005945 {source="TAO"} ! neurocranial trabecula -relationship: dubious_for_taxon NCBITaxon:8292 {editor_note="check AAO"} ! Amphibia +relationship: dubious_for_taxon NCBITaxon:8292 {comment="EDITOR_NOTE check AAO"} ! Amphibia relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: overlaps UBERON:0001703 {source="TAO"} ! neurocranium relationship: part_of UBERON:0002241 {source="TAO"} ! chondrocranium @@ -151884,7 +151884,7 @@ xref: SCTID:361795009 xref: Wikipedia:Malleolus is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0004410 ! distal epiphysis of fibula -property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", seeAlso="UBERON:0004410", source="UBERON:skansa"} +property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", source="UBERON:skansa", seeAlso="UBERON:0004410"} [Term] id: UBERON:0012292 @@ -159006,6 +159006,7 @@ relationship: part_of UBERON:0001737 ! larynx id: UBERON:0014374 name: embryoid body def: "Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells." [EFO:0004988, https://github.com/obophenotype/uberon/issues/245] +comment: EDITOR_NOTE in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology subset: efo_slim synonym: "embryonic body" RELATED [Wikipedia:Embryoid_body] xref: BTO:0001718 @@ -159014,7 +159015,6 @@ xref: MESH:D058732 xref: Wikipedia:Embryoid_body is_a: UBERON:0002050 {source="EFO"} ! embryonic structure relationship: composed_primarily_of CL:0002248 {source="Wikipedia"} ! pluripotent stem cell -property_value: editor_note "in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology" xsd:string property_value: external_definition "Embryoid bodies are structures resembling embryos, occurring in several types of germ cell tumors[BTO]." xsd:string {reference="Dorlands_Medical_Dictionary:MerckSource", source="BTO:0001718"} [Term] @@ -181506,7 +181506,7 @@ id: UBERON:0034930 name: auricular feather intersection_of: UBERON:0000022 ! feather intersection_of: surrounds UBERON:0001691 ! external ear -relationship: has_quality PATO:0001297 {editor_note="request more specific terms from PATO"} ! reflectivity +relationship: has_quality PATO:0001297 {comment="EDITOR_NOTE request more specific terms from PATO"} ! reflectivity property_value: function_notes "the auricular feathers play a role in hearing by reflecting and funneling sound into the external acoustic meatus" xsd:string [Term] @@ -223935,7 +223935,7 @@ property_value: dcterms-date "2022-10-31T07:56:47Z" xsd:dateTime id: UBERON:8480041 name: testicular sheath def: "Bilayer sheath that covers both the insect male mature gonad and a portion of genital disc-derived structures. It is composed of an outer pigment cell layer, an inner muscle cell layer, and their respective basal laminae." [PMID:9553045] -synonym: "testis sheath" EXACT [] {http://purl.obolibrary.org/obo/IAO_0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} +synonym: "testis sheath" EXACT [] {comment="CURATOR NOTE https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} is_a: UBERON:0004923 ! organ component layer relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli relationship: in_taxon NCBITaxon:50557 ! Insecta